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Finding gene length

Hello everyone

I have RNA seq data and I would like to find gene length. I used Tophat and Bowtie to get cufflinks. Any idea about how to count gene length.

Thanks for help

rna-seq r
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updated by h.mon h.mon • written by saj98 saj98

1 answer

EDIT: here is the answer to what the OP really wants to do.

This page has a simple formula to convert FPKM to TPM. You may use the R function fpkmToTpm() to perform the conversion, available at this repository. The function is so short I can copy it here:

fpkmToTpm <- function(x)
{
    lDenom <- log(sum(x))
    exp(log(x) - lDenom + log(1e6))
}

Old answer: See "Output formats used in the Cufflinks suite", some output files include transcript length.

P.S.: and please rewrite your question to make it more clear.

• 0 views • link
written by h.mon h.mon

my question How I can get gene length? I am looking for gene length to calculate TPM value instead of FPKM value. Is that clear?

• 0 views • link
written by saj98 saj98

More or less clear what you want, totally unclear what you did so far. Did you run cufflinks? How did you run cufflinks? Did you see cufflinks outputs transcript length?

• 0 views • link
written by h.mon h.mon

Here is what I got from cuufflinks:

setwd("D:/PHD thesisi/diff_out") cuff <- readCufflinks() cuff CuffSet instance with: 2 samples 55004 genes 94479 isoforms 72846 TSS 27521 CDS 55004 promoters 72846 splicing 21901 relCDS Thanks for your help and sorry for confusing

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written by saj98 saj98

See my updated answer, you do not need the gene lengths for the conversion.

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written by h.mon h.mon

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